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Ambiguity in specification on how to handle lesion "masks" (or segmentations?)

Open yarikoptic opened this issue 3 years ago • 0 comments

Complimentary to #174 although less concerned with placement and either lesions could be considered raw or derivative data (IMHO everything is derivative ;) )

ATM lesions are mentioned in two places:

  • https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#masks -- so be stored in _mask.nii.gz with .json containing "Type": "Lesion"
  • https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#segmentations -- so to be stored in _dseg.nii.gz (I guess).

For a BIDS newbee, or oldbee like me, it is not clear which one I should use if I am to store a lesion mask/segmentation. I guess I would resort to "segmentation" if in the same volume I would like to have multiple "objects" or lesions reported, but if I need just a singular one, I better go for a _mask.

  • Is that the right logic?
  • Should we make it a bit more explicit within specification as some kind of guidance?

edit: in part inspired by incorrect use of elderly _roi while taking fmriprep docs as guiding light. Fix to those submitted in https://github.com/nipreps/fmriprep/pull/2715

yarikoptic avatar Feb 15 '22 16:02 yarikoptic